From 7595475f40b6caa80e43d2228c340d5ede187a9e Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 10 Oct 2019 12:05:55 +0200
Subject: [PATCH] Write contig name as i005 instead of 005i

---
 .../general_format_functions.py               |    3 +-
 .../exp_files/res_test_write_geneCDS.lst      |    2 +-
 .../exp_files/res_test_write_geneCRISPR.lst   |    2 +-
 .../test_annotate/test_format_func.py         | 2182 ++++++++---------
 4 files changed, 1085 insertions(+), 1104 deletions(-)

diff --git a/PanACoTA/annotate_module/general_format_functions.py b/PanACoTA/annotate_module/general_format_functions.py
index 1ec1caf1..fec88241 100644
--- a/PanACoTA/annotate_module/general_format_functions.py
+++ b/PanACoTA/annotate_module/general_format_functions.py
@@ -165,7 +165,6 @@ def handle_genome(args):
         format_one_genome = fprodigal.format_one_genome
     else:
         format_one_genome = fprokka.format_one_genome
-
     # Set logger for this process
     qh = logging.handlers.QueueHandler(q)
     root = logging.getLogger()
@@ -234,7 +233,7 @@ def write_gene(gtype, locus_num, gene_name, product, crispr_num, cont_loc,
         gene_name = "crispr"
         product = "crispr-array"
         crispr_num += 1
-    locus_name = "{}.{}{}_{}".format(genome, str(cont_num).zfill(4), cont_loc,
+    locus_name = "{}.{}{}_{}".format(genome, cont_loc, str(cont_num).zfill(4),
                                      str(locus_num).zfill(5))
     # If '|' character found in those fields, replace by '_' to avoid problems while parsing
     more_info = "| {} | {} | {} | {}".format(product.replace("|", "_"),
diff --git a/test/data/annotate/exp_files/res_test_write_geneCDS.lst b/test/data/annotate/exp_files/res_test_write_geneCDS.lst
index fd07c103..36277635 100755
--- a/test/data/annotate/exp_files/res_test_write_geneCDS.lst
+++ b/test/data/annotate/exp_files/res_test_write_geneCDS.lst
@@ -1 +1 @@
-154	656	C	CDS	ESCO.0216.00005.i0015_5621221	abc	| new product | 454.12.5 | more information... dfd _ with _ pipe_characters...
+154	656	C	CDS	ESCO.0216.00005.i0015_5621221	abc	| new product | 454.12.5 | more information... dfd _ with _ pipe_characters... | mydb_pipe
diff --git a/test/data/annotate/exp_files/res_test_write_geneCRISPR.lst b/test/data/annotate/exp_files/res_test_write_geneCRISPR.lst
index 8fc5046e..47336e11 100755
--- a/test/data/annotate/exp_files/res_test_write_geneCRISPR.lst
+++ b/test/data/annotate/exp_files/res_test_write_geneCRISPR.lst
@@ -1 +1 @@
-154	656	D	CRISPR	ESCO.0216.00005.b0015_CRISPR1	crispr	| crispr-array | NA | more information... dfd _ with _ pipe_characters...
+154	656	D	CRISPR	ESCO.0216.00005.b0015_CRISPR1	crispr	| crispr-array | NA | more information... dfd _ with _ pipe_characters... | mydb_pipe
diff --git a/test/test_unit/test_annotate/test_format_func.py b/test/test_unit/test_annotate/test_format_func.py
index b4ecbaf3..c4e1bafc 100755
--- a/test/test_unit/test_annotate/test_format_func.py
+++ b/test/test_unit/test_annotate/test_format_func.py
@@ -2,14 +2,14 @@
 # coding: utf-8
 
 """
-Unit tests for format_functions.py
+Unit tests for general_format_functions.py
 """
 
 import os
 import logging
 import shutil
 from io import StringIO
-import PanACoTA.annotate_module.format_functions as ffunc
+import PanACoTA.annotate_module.general_format_functions as ffunc
 import PanACoTA.utils as utils
 
 
@@ -22,7 +22,7 @@ def my_logger():
     m = multiprocessing.Manager()
     q = m.Queue()
     qh = logging.handlers.QueueHandler(q)
-    root = logging.getLogger()
+    root = logging.getLogger('test_gene-format')
     root.setLevel(logging.DEBUG)
     root.handlers = []
     logging.addLevelName(utils.detail_lvl(), "DETAIL")
@@ -46,20 +46,24 @@ def test_write_gene():
     cont_num = 15
     ecnum = "454.12.5"
     inf2 = "more information... dfd | with | pipe|characters..."
+    db_xref = "mydb|pipe"
     strand = "C"
-    start = 154
-    end = 656
+    start = str(154)
+    end = str(656)
     lstfile = "toto.lst"
     lstopenfile = open(lstfile, "w")
-    res = ffunc.write_gene(gtype, locus_num, gene_name, product, crispr_num,
-                           cont_loc, genome, cont_num, ecnum, inf2, strand,
-                           start, end, lstopenfile)
+    crispres, lst_line = ffunc.write_gene(gtype, locus_num, gene_name, product, crispr_num,
+                                          cont_loc, genome, cont_num, ecnum, inf2, db_xref, strand,
+                                          start, end, lstopenfile)
     lstopenfile.close()
     exp_file = os.path.join("test", "data", "annotate", "exp_files", "res_test_write_geneCDS.lst")
-    assert res == crispr_num
+    assert crispres == crispr_num
     with open(exp_file, "r") as expf, open(lstfile, "r") as lstf:
         for line_exp, line_out in zip(expf, lstf):
             assert line_exp == line_out
+    assert lst_line == ("154\t656\tC\tCDS\tESCO.0216.00005.i0015_5621221\tabc\t| new product "
+                        "| 454.12.5 | more information... dfd _ with _ pipe_characters... | "
+                        "mydb_pipe")
     os.remove(lstfile)
 
 
@@ -78,1107 +82,1085 @@ def test_write_crispr():
     cont_num = 15
     ecnum = "NA"
     inf2 = "more information... dfd | with | pipe|characters..."
+    db_xref = "mydb|pipe"
     strand = "D"
-    start = 154
-    end = 656
+    start = str(154)
+    end = str(656)
     lstfile = "toto.lst"
     lstopenfile = open(lstfile, "w")
-    res = ffunc.write_gene(gtype, locus_num, gene_name, product, crispr_num,
-                           cont_loc, genome, cont_num, ecnum, inf2, strand,
-                           start, end, lstopenfile)
+    crispres, lstline = ffunc.write_gene(gtype, locus_num, gene_name, product, crispr_num,
+                                         cont_loc, genome, cont_num, ecnum, inf2, db_xref, strand,
+                                         start, end, lstopenfile)
     lstopenfile.close()
     exp_file = os.path.join("test", "data", "annotate", "exp_files",
                             "res_test_write_geneCRISPR.lst")
-    assert res == 2
+    assert crispres == 2
     with open(exp_file, "r") as expf, open(lstfile, "r") as lstf:
         for line_exp, line_out in zip(expf, lstf):
+            print(f"\n{line_out}\n{line_exp}")
             assert line_exp == line_out
+    assert lstline == ("154\t656\tD\tCRISPR\tESCO.0216.00005.b0015_CRISPR1\tcrispr\t| "
+                       "crispr-array | NA | more information... dfd _ with _ pipe_characters... | "
+                       "mydb_pipe")
     os.remove(lstfile)
 
 
-def test_tbl_to_lst():
-    """
-    Check that generated lstinfo file is as expected, when the genome name is the same as
-    it already was in the genome given to prokka.
-    The test tblfile contains the following aspects:
-    - gene in D strand (start < end)
-    - gene in C strand (start > end)
-    - CDS features (some with all info = ECnumber, gene name, product etc. ;
-    some with missing info)
-    - tRNA type
-    - repeat_region type (*2)
-    - contigs with more than 2 genes
-    - contig with only 2 genes (both 'b' loc)
-    - contig with 1 gene ('b' loc)
-    - contig without gene (should be skipped)
-    """
-    tblfile = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
-                           "prokka_out_for_test.tbl")
-    lstfile = os.path.join("test", "data", "annotate", "test_tbl2lst.lst")
-    exp_lst = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    name = "test.0417.00002"
-    assert ffunc.tbl2lst(tblfile, lstfile, name)
-    with open(exp_lst, "r") as expf, open(lstfile, "r") as lstf:
-        for line_exp, line_out in zip(expf, lstf):
-            assert line_exp == line_out
-    os.remove(lstfile)
-
-
-def test_tbl_to_lst_new_name():
-    """
-    Check that generated lstinfo file is as expected, when the genome name has changed between
-    the one given to prokka, and the name given now.
-    The test tblfile contains the following aspects:
-    - gene in D strand (start < end)
-    - gene in C strand (start > end)
-    - CDS features (some with all info = ECnumber, gene name, product etc. ;
-    some with missing info)
-    - tRNA type
-    - repeat_region type (*2)
-    - contigs with more than 2 genes
-    - contig with only 2 genes (both 'b' loc)
-    - contig with 1 gene ('b' loc)
-    - contig without gene (should be skipped)
-    """
-    tblfile = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
-                           "prokka_out_for_test.tbl")
-    lstfile = os.path.join("test", "data", "annotate", "test_tbl2lstNewName.lst")
-    exp_lst = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst-newName.lst")
-    name = "test.0417.00010"
-    assert not ffunc.tbl2lst(tblfile, lstfile, name)
-    with open(exp_lst, "r") as expf, open(lstfile, "r") as lstf:
-        for line_exp, line_out in zip(expf, lstf):
-            assert line_exp == line_out
-    os.remove(lstfile)
-
-
-def test_write_header_gene():
-    """
-    From a given line of lstinfo file, giving info for a gene (start, end, gene name,
-    product, EC number, more information), check that the header line of the protein and
-    gene files are generated as expected.
-    """
-    outfile = StringIO()
-    lstline = ("4416\t6068\tD\tCDS\ttest.0417.00002.i0001_00005\tyiaD\t| "
-               "putative lipoprotein YiaD | 6.3.2.- | similar to AA sequence:UniProtKB:P37665")
-    ffunc.write_header(lstline, outfile)
-    res = outfile.getvalue()
-    exp = (">test.0417.00002.i0001_00005 1653 yiaD | putative lipoprotein YiaD | 6.3.2.- "
-           "| similar to AA sequence:UniProtKB:P37665\n")
-    assert res == exp
-    outfile.close()
-
-
-def test_write_header_gene_no_name():
-    """
-    From a given line of lstinfo file, giving info for a gene with many unknown parts (gene
-    name, product, EC number and more information are NAs), check that the header line of the
-    protein and gene files are generated as expected.
-    """
-    outfile = StringIO()
-    lstline = ("4632\t5000\tC\tCDS\ttest.0417.00002.b0002_00011\tNA\t| hypothetical protein "
-               "| NA | NA")
-    ffunc.write_header(lstline, outfile)
-    res = outfile.getvalue()
-    exp = ">test.0417.00002.b0002_00011 369 NA | hypothetical protein | NA | NA\n"
-    assert res == exp
-    outfile.close()
-
-
-def test_write_header_crispr():
-    """
-    From a given line of lstinfo file, giving info for a CRISPR check that the header
-    line of the protein and gene files are generated as expected.
-    """
-    outfile = StringIO()
-    lstline = ("296902\t2968265\tC\tCRISPR\ttest.0417.00002.b0003_CRISPR1\tcrispr\t| "
-               "crispr-array | NA | NA")
-    ffunc.write_header(lstline, outfile)
-    res = outfile.getvalue()
-    exp = ">test.0417.00002.b0003_CRISPR1 2671364 crispr | crispr-array | NA | NA\n"
-    assert res == exp
-    outfile.close()
-
-
-def test_create_prt_wrong_header_sep():
-    """
-    Test that, when creating prt file from faa and lst, if a header of faa file is
-    not in the right format (protein name and number are not separated by '_'),
-    it writes an error, erases prt file, and returns False.
-    """
-    logger = my_logger()
-    faaseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-wrongHeaderSep.faa")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    prtseq = os.path.join("test", "data", "annotate", "test_create_prt-wrongHeadSep.prt")
-    assert not ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
-    assert not os.path.isfile(prtseq)
-    msg = ("Unknown header format >JGIKIPIJ00008 in test/data/annotate/test_files/"
-           "prokka_out_for_test-wrongHeaderSep.faa. Error: invalid literal for int() "
-           "with base 10: '>JGIKIPIJ00008'\nPrt file not created from "
-           "test/data/annotate/test_files/prokka_out_for_test-wrongHeaderSep.faa.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_prt_wrong_header_int():
-    """
-    Test that, when creating prt file from faa and lst, if a header of faa file is
-    not in the right format (protein name and number are separated by '_', but protein num
-    contains a letter), it writes an error, erases prt file, and returns False.
-    """
-    logger = my_logger()
-    faaseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-wrongHeaderInt.faa")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    prtseq = os.path.join("test", "data", "annotate", "test_create_prt-wrongHeadInt.prt")
-    assert not ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
-    assert not os.path.isfile(prtseq)
-    msg = ("Unknown header format >JGIKIPIJ_d0008 in test/data/annotate/test_files/"
-           "prokka_out_for_test-wrongHeaderInt.faa. Error: invalid literal for int() "
-           "with base 10: 'd0008'\nPrt file not created from "
-           "test/data/annotate/test_files/prokka_out_for_test-wrongHeaderInt.faa.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_prt_miss_lst():
-    """
-    Test that, when creating prt file from faa and lst, if a protein of faa file is not present in
-    the lst file, it writes an error, removes the prt file, and returns False.
-    """
-    logger = my_logger()
-    faaseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-supHeader.faa")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    prtseq = os.path.join("test", "data", "annotate", "test_create_prt-missLst.prt")
-    assert not ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
-    assert not os.path.isfile(prtseq)
-    msg = ("Missing info for protein >sup-prot_00012 in "
-           "test/data/annotate/exp_files/res_tbl2lst.lst. If it is "
-           "actually present in the lst file, check that proteins are ordered by "
-           "increasing number in both lst and faa files.\n"
-           "Prt file not created from test/data/annotate/test_files/"
-           "prokka_out_for_test-supHeader.faa.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_prt_wrong_order():
-    """
-    Test that, when creating prt file from faa and lst, if a protein of faa file is not in
-    increasing protein number, so that it does not correspond to the protein in the lstinfo file,
-    it writes an error, removes the prt file, and returns False.
-    """
-    logger = my_logger()
-    faaseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-wrongOrder.faa")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    prtseq = os.path.join("test", "data", "annotate", "test_create_prt-wrongOrder.prt")
-    assert not ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
-    assert not os.path.isfile(prtseq)
-    msg = ("Missing info for protein >appears_after_13_00011 in "
-           "test/data/annotate/exp_files/res_tbl2lst.lst. If it is "
-           "actually present in the lst file, check that proteins are ordered by "
-           "increasing number in both lst and faa files.\n"
-           "Prt file not created from test/data/annotate/test_files/"
-           "prokka_out_for_test-wrongOrder.faa.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_prt_ok():
-    """
-    Test that when everything is ok in both faa and lst files, the prt file is
-    created as expected.
-    """
-    logger = my_logger()
-    faaseq = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
-                          "prokka_out_for_test.faa")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    prtseq = os.path.join("test", "data", "annotate", "test_create_prt.prt")
-    assert ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
-    exp_file = os.path.join("test", "data", "annotate", "exp_files", "res_create_prt.faa")
-    with open(exp_file, "r") as expf, open(prtseq, "r") as prtf:
-        for line_exp, line_out in zip(expf, prtf):
-            assert line_exp == line_out
-    os.remove(prtseq)
-
-
-def test_create_gen_sup_crispr():
-    """
-    Test that when there is a CRISPR in the ffn file, but not in lstinfo,
-    it generates an error, because the CRISPR ID does not correspond to the gene ID in lstinfo.
-    It should return False, write an error message, and remove the .gen file.
-    Moreover, the CRISPR ID is not in the same format as a gene ID, so the error should
-    be on the format.
-    """
-    logger = my_logger()
-    ffnseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-supCRISPR.ffn")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    genseq = os.path.join("test", "data", "annotate", "test_create_gen_supCRISPR.gen")
-    assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
-    assert not os.path.isfile(genseq)
-    msg = ("Unknown header format >prokka_out_for_test in test/data/annotate/test_files/"
-           "prokka_out_for_test-supCRISPR.ffn.\nGen file will not be created.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_gen_sup_gene():
-    """
-    Test that, when creating gen file from ffn and lst, if a gene of ffn file is not present in
-    the lst file, it writes an error, removes the gen file, and returns False.
-    """
-    logger = my_logger()
-    ffnseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-supGene.ffn")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    prtseq = os.path.join("test", "data", "annotate", "test_create_gen-supgene.prt")
-    assert not ffunc.create_gen(ffnseq, lstfile, prtseq, logger[1])
-    assert not os.path.isfile(prtseq)
-    msg = ("Missing info for gene >sup_gene_00012 in test/data/annotate/exp_files/"
-           "res_tbl2lst.lst. If it is actually present "
-           "in the lst file, check that genes are ordered by increasing "
-           "number in both lst and ffn files.\nGen file not created"
-           " from test/data/annotate/test_files/prokka_out_for_test-supGene.ffn.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_gen_miss_crispr():
-    """
-    Test for situation where there are 2 CRISPRs in the lstinfo file, the first one
-    is not in the ffn file, while the second one is in the ffn file.
-    It should return an error message about CRISPR number not corresponding, as
-    the first CRISPR found in ffn (CRISPR 1) corresponds to CRISPR2 in lstinfo file.
-    Gene file should be removed, and the function should return False
-    """
-    logger = my_logger()
-    ffnseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-missCRISPR.ffn")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    genseq = os.path.join("test", "data", "annotate", "test_create_gen_missCRISPR.gen")
-    assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
-    assert not os.path.isfile(genseq)
-    msg = ("Problem with CRISPR numbers in test/data/annotate/exp_files/res_tbl2lst.lst. "
-           "CRISPR >prokka_out_for_test in ffn is CRISPR num 1, whereas it is annotated "
-           "as CRISPR num 2 in lst file.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_gen_no_crispr_ffn():
-    """
-    Test that when the there is a CRISPR in the lst file, but not in the ffn file,
-    everything goes well, as in some versions of prokka (1.12)n CRISPRs are not in ffn while
-    they are specified in lst. Function should return True, and gene file created.
-    """
-    ffnseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-noCRISPRffn.ffn")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    genseq = os.path.join("test", "data", "annotate", "test_create_gen_noCRISPRffn.gen")
-    assert ffunc.create_gen(ffnseq, lstfile, genseq, my_logger()[1])
-    assert os.path.isfile(genseq)
-    exp_file = os.path.join("test", "data", "annotate", "exp_files",
-                            "res_create_gen_noCRISPRffn.gen")
-    with open(exp_file, "r") as expf, open(genseq, "r") as prtf:
-        for line_exp, line_out in zip(expf, prtf):
-            assert line_exp == line_out
-    os.remove(genseq)
-
-
-def test_create_gen_wrong_header_sep():
-    """
-    Test that, when creating gen file from ffn and lst, if a header of ffn file is
-    not in the right format (gene name and number are not separated by '_'),
-    it writes an error, erases gen file, and returns False.
-    """
-    logger = my_logger()
-    ffnseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-wrongFormat.ffn")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    genseq = os.path.join("test", "data", "annotate", "test_create_gen_wrongHeadSep.gen")
-    assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
-    assert not os.path.isfile(genseq)
-    msg = ("Unknown header format >JGIKIPIJ-00005 in test/data/annotate/test_files/"
-           "prokka_out_for_test-wrongFormat.ffn.\n"
-           "Gen file will not be created.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_gen_wrong_header_int():
-    """
-    Test that, when creating gen file from ffn and lst, if a header of ffn file is
-    not in the right format (gene name and number are separated by '_', but gene num
-    contains a letter), it writes an error, erases gen file, and returns False.
-    """
-    logger = my_logger()
-    ffnseq = os.path.join("test", "data", "annotate", "test_files",
-                          "prokka_out_for_test-wrongInt.ffn")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    genseq = os.path.join("test", "data", "annotate", "test_create_gen_wrongHeadInt.gen")
-    assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
-    assert not os.path.isfile(genseq)
-    msg = ("Unknown header format >JGIKIPIJ_a00005 in test/data/annotate/test_files/"
-           "prokka_out_for_test-wrongInt.ffn.\n"
-           "Gen file will not be created.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_gen_wrong_lst_int():
-    """
-    Test that, when creating gen file from ffn and lst, if a gene name in lst file is
-    not in the right format (gene name and number are separated by '_', but gene num
-    contains a letter), it writes an error, erases gen file, and returns False.
-    Because the gene name in ffn won't be found in lst (a it contains an error in lst).
-    """
-    logger = my_logger()
-    ffnseq = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
-                          "prokka_out_for_test.ffn")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst-wrongGeneName.lst")
-    genseq = os.path.join("test", "data", "annotate", "test_create_gen_wrongLstHeadInt.gen")
-    assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
-    assert not os.path.isfile(genseq)
-    msg = ("Missing info for gene >JGIKIPIJ_00009 in test/data/annotate/exp_files/"
-           "res_tbl2lst-wrongGeneName.lst. If it is actually present "
-           "in the lst file, check that genes are ordered by increasing "
-           "number in both lst and ffn files.\nGen file not created "
-           "from test/data/annotate/test_files/original_name.fna-prokkaRes/"
-           "prokka_out_for_test.ffn.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-
-
-def test_create_gen_ok():
-    """
-    Test that when everything is ok in both ffn and lst files, the gen file is
-    created as expected.
-    """
-    faaseq = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
-                          "prokka_out_for_test.ffn")
-    lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
-    genseq = os.path.join("test", "data", "annotate", "test_create_gen.gen")
-    assert ffunc.create_gen(faaseq, lstfile, genseq, my_logger()[1])
-    exp_file = os.path.join("test", "data", "annotate", "exp_files", "res_create_gen.gen")
-    with open(exp_file, "r") as expf, open(genseq, "r") as prtf:
-        for line_exp, line_out in zip(expf, prtf):
-            assert line_exp == line_out
-    os.remove(genseq)
-
-
-def test_handle_line_gff():
-    """
-    Check that given a line in lstinfo with no information (gene name, ecnumber, product,
-    inference), it returns the good gff line
-    """
-    line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tNA\t"
-                "| NA | NA | NA")
-    line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
-                "ID=ONKACNIE_00001;inference=ab initio "
-                "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
-    outgff = "test_handle_line_gff.gff"
-    gfff = open(outgff, "w")
-    ffunc.handle_line_gff(line_lst, line_gff, gfff)
-    gfff.close()
-    with open(outgff, "r") as gf:
-        lines = gf.readlines()
-        assert len(lines) == 1
-        exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
-                    "ID=ESCO.1015.00001.b0001_00001;locus_tag=ESCO.1015.00001.b0001_00001\n")
-        assert lines[0] == exp_line
-    os.remove(outgff)
-
-
-def test_handle_line_gff_ecnum():
-    """
-    Check that given a line in lstinfo with only ec_number information,
-    it returns the good gff line
-    """
-    line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tNA\t"
-                "| NA | 123.995.4546 | NA")
-    line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
-                "ID=ONKACNIE_00001;inference=ab initio "
-                "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
-    outgff = "test_handle_line_gff-ecnum.gff"
-    gfff = open(outgff, "w")
-    ffunc.handle_line_gff(line_lst, line_gff, gfff)
-    gfff.close()
-    with open(outgff, "r") as gf:
-        lines = gf.readlines()
-        assert len(lines) == 1
-        exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
-                    "ID=ESCO.1015.00001.b0001_00001;eC_number=123.995.4546;"
-                    "locus_tag=ESCO.1015.00001.b0001_00001\n")
-        assert lines[0] == exp_line
-    os.remove(outgff)
-
-
-def test_handle_line_gff_gene():
-    """
-    Check that given a line in lstinfo with only gene name information,
-    it returns the good gff line
-    """
-    line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tge4a\t"
-                "| NA | NA | NA")
-    line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
-                "ID=ONKACNIE_00001;inference=ab initio "
-                "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
-    outgff = "test_handle_line_gff-gene.gff"
-    gfff = open(outgff, "w")
-    ffunc.handle_line_gff(line_lst, line_gff, gfff)
-    gfff.close()
-    with open(outgff, "r") as gf:
-        lines = gf.readlines()
-        assert len(lines) == 1
-        exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
-                    "ID=ESCO.1015.00001.b0001_00001;Name=ge4a;gene=ge4a;"
-                    "locus_tag=ESCO.1015.00001.b0001_00001\n")
-        assert lines[0] == exp_line
-    os.remove(outgff)
-
-
-def test_handle_line_gff_inf():
-    """
-    Check that given a line in lstinfo with only inference information,
-    it returns the good gff line
-    """
-    line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tNA\t"
-                "| NA | NA | ab initio prediction:Prodigal:2.6")
-    line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
-                "ID=ONKACNIE_00001;inference=ab initio "
-                "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
-    outgff = "test_handle_line_gff-inf.gff"
-    gfff = open(outgff, "w")
-    ffunc.handle_line_gff(line_lst, line_gff, gfff)
-    gfff.close()
-    with open(outgff, "r") as gf:
-        lines = gf.readlines()
-        assert len(lines) == 1
-        exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
-                    "ID=ESCO.1015.00001.b0001_00001;inference=ab initio "
-                    "prediction:Prodigal:2.6;locus_tag=ESCO.1015.00001.b0001_00001\n")
-        assert lines[0] == exp_line
-    os.remove(outgff)
-
-
-def test_handle_line_gff_prod():
-    """
-    Check that given a line in lstinfo with only product information,
-    it returns the good gff line
-    """
-    line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tNA\t"
-                "| hypothetical protein | NA | NA")
-    line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
-                "ID=ONKACNIE_00001;inference=ab initio "
-                "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
-    outgff = "test_handle_line_gff-prod.gff"
-    gfff = open(outgff, "w")
-    ffunc.handle_line_gff(line_lst, line_gff, gfff)
-    gfff.close()
-    with open(outgff, "r") as gf:
-        lines = gf.readlines()
-        assert len(lines) == 1
-        exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
-                    "ID=ESCO.1015.00001.b0001_00001;locus_tag=ESCO.1015.00001.b0001_00001;"
-                    "product=hypothetical protein\n")
-        assert lines[0] == exp_line
-    os.remove(outgff)
-
-
-def test_generate_gff():
-    """
-    Test creating gff file.
-    """
-    prokgff = os.path.join("test", "data", "annotate", "test_files", "prokka_out_gff.gff")
-    gffout = os.path.join("test", "data", "annotate", "test_creategff.gff")
-    lstgenome = os.path.join("test", "data", "annotate", "test_files", "lstinfo_for_gff.lst")
-    assert ffunc.generate_gff(prokgff, gffout, lstgenome, my_logger()[1])
-    exp_gff = os.path.join("test", "data", "annotate", "exp_files", "res_create_gff.gff")
-    with open(gffout, "r") as gffo, open(exp_gff, "r") as expf:
-        for line_exp, line_out in zip(expf, gffo):
-            assert line_exp == line_out
-    os.remove(gffout)
-
-
-def test_generate_gff_error():
-    """
-    Test creating gff file.
-    """
-    logger = my_logger()
-    prokgff = os.path.join("test", "data", "annotate", "test_files", "prokka_out_gff-error.gff")
-    lstgenome = os.path.join("test", "data", "annotate", "test_files", "lstinfo_for_gff.lst")
-    gffout = os.path.join("test", "data", "annotate", "test_creategff.gff")
-    assert not ffunc.generate_gff(prokgff, gffout, lstgenome, logger[1])
-    os.remove(gffout)
-    q = logger[0]
-    assert q.qsize() == 1
-    logfound = q.get()
-    msg = ("Problem with your gff file. '##FASTA' is not a gff entry line, whereas it should "
-           "correspond to '863\t1795\tD\tCDS\tESCO.1015.00001.b0003_00016\tNA\t"
-           "| hypothetical protein | NA | NA'")
-    assert msg in logfound.message
-    assert logfound.levelname == "ERROR"
-
-
-def test_handle_genome_nores():
-    """
-    Test that when we try to format a genome which is not in results,
-    it returns a tuple with "no_res" and the genome name.
-    """
-    results = {"abcd.fasta": True}
-    args = ("toto.fasta", "name", "genome/path", "prokka/path", "lst/dir", "prot/dir",
-            "gene/dir", "rep/dir", "gff/dir", results, my_logger()[0])
-    res = ffunc.handle_genome(args)
-    assert res == ("no_res", "toto.fasta")
-
-
-def test_handle_genome_badprok():
-    """
-    Test that when we try to format a genome which is in results, but with False,
-    it returns a tuple with "bad_prokka" and the genome name.
-    """
-    results = {"abcd.fasta": True, "toto.fasta": False}
-    args = ("toto.fasta", "name", "genome/path", "prokka/path", "lst/dir", "prot/dir",
-            "gene/dir", "rep/dir", "gff/dir", results, my_logger()[0])
-    res = ffunc.handle_genome(args)
-    assert res == ("bad_prokka", "toto.fasta")
-
-
-def test_handle_genome_formatok():
-    """
-    Test that when we try to format a genome which is in results, with True,
-    it returns a tuple with "True" and the genome name.
-    """
-    gpath = os.path.join("test", "data", "annotate", "genomes",
-                         "B2_A3_5.fasta-split5N.fna-short-contig.fna")
-    name = "test.0417.00002"
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    lst_dir = os.path.join("test", "data", "annotate")
-    prot_dir = lst_dir
-    gene_dir = lst_dir
-    rep_dir = lst_dir
-    gff_dir = lst_dir
-    results = {"B2_A3_5.fasta-split5N.fna-short-contig.fna": True, "toto.fasta": False}
-    args = ("B2_A3_5.fasta-split5N.fna-short-contig.fna", name, gpath, prok_path,
-            lst_dir, prot_dir,
-            gene_dir, rep_dir, gff_dir, results, my_logger()[0])
-    res = ffunc.handle_genome(args)
-    assert res == (True, "B2_A3_5.fasta-split5N.fna-short-contig.fna")
-    os.remove(os.path.join(lst_dir, name + ".prt"))
-    os.remove(os.path.join(lst_dir, name + ".fna"))
-    os.remove(os.path.join(lst_dir, name + ".gen"))
-    os.remove(os.path.join(lst_dir, name + ".lst"))
-    os.remove(os.path.join(lst_dir, name + ".gff"))
-
-
-def test_handle_genome_formaterror():
-    """
-    Test that when we try to format a genome which is in results, but with False,
-    it returns a tuple with "bad_prokka" and the genome name.
-    """
-    logger = my_logger()
-    gpath = os.path.join("test", "data", "annotate", "genomes",
-                         "B2_A3_5.fasta-problems.fna-short-contig.fna")
-    name = "test.0417.00002"
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".tbl")
-    tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".tbl")
-    shutil.copyfile(tbl_init, tblout)
-    gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".gff")
-    gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".gff")
-    shutil.copyfile(gff_init, gffout)
-    lst_dir = os.path.join("test", "data", "annotate")
-    prot_dir = lst_dir
-    gene_dir = lst_dir
-    rep_dir = lst_dir
-    gff_dir = lst_dir
-    results = {"B2_A3_5.fasta-problems.fna-short-contig.fna": True, "toto.fasta": False}
-    args = ("B2_A3_5.fasta-problems.fna-short-contig.fna", name, gpath,
-            prok_path, lst_dir, prot_dir, gene_dir, rep_dir, gff_dir, results, logger[0])
-    res = ffunc.handle_genome(args)
-    assert res == (False, "B2_A3_5.fasta-problems.fna-short-contig.fna")
-    msg = ("Unknown header format >EPKOMDHM_i00002 hypothetical protein in "
-           "test/data/annotate/exp_files/B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes/"
-           "test.0417.00002.ffn.\n"
-           "Gen file will not be created.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-    # remove tblout which was copied for this test
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".prt"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".gen"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".fna"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".lst"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".gff"))
-    os.remove(tblout)
-    os.remove(gffout)
-
-
-def test_format1genome():
-    """
-    Test that formatting a genome (making .prt, .gen, .fna, .lst) works, with a genome
-    which did not change name between prokka run and format step.
-    """
-    gpath = os.path.join("test", "data", "annotate", "genomes",
-                         "B2_A3_5.fasta-split5N.fna-short-contig.fna")
-    name = "test.0417.00002"
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    lst_dir = os.path.join("test", "data", "annotate")
-    prot_dir = lst_dir
-    gene_dir = lst_dir
-    rep_dir = lst_dir
-    gff_dir = lst_dir
-    assert ffunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir,
-                                   gene_dir, rep_dir, gff_dir, my_logger()[1])
-    # Check that all files were created
-    assert os.path.isfile(os.path.join(lst_dir, name + ".lst"))
-    assert os.path.isfile(os.path.join(lst_dir, name + ".fna"))
-    assert os.path.isfile(os.path.join(lst_dir, name + ".prt"))
-    assert os.path.isfile(os.path.join(lst_dir, name + ".gen"))
-    assert os.path.isfile(os.path.join(lst_dir, name + ".gff"))
-    # Check the contents of the files
-    explst = os.path.join(prok_path, "res_format-B2.lst")
-    expprt = os.path.join(prok_path, "res_format-B2.prt")
-    expgen = os.path.join(prok_path, "res_format-B2.gen")
-    expgff = os.path.join(prok_path, "res_format-B2.gff")
-    with open(explst, "r") as lstf, open(os.path.join(lst_dir, name + ".lst"), "r") as lsto:
-        for line_exp, line_out in zip(lstf, lsto):
-            assert line_exp == line_out
-    with open(expprt, "r") as expf, open(os.path.join(lst_dir, name + ".prt"), "r") as outf:
-        for line_exp, line_out in zip(expf, outf):
-            assert line_exp == line_out
-    with open(expgen, "r") as expf, open(os.path.join(lst_dir, name + ".gen"), "r") as outf:
-        for line_exp, line_out in zip(expf, outf):
-            assert line_exp == line_out
-    with open(gpath, "r") as expf, open(os.path.join(lst_dir, name + ".fna"), "r") as outf:
-        for line_exp, line_out in zip(expf, outf):
-            assert line_exp == line_out
-    with open(expgff, "r") as expf, open(os.path.join(lst_dir, name + ".gff"), "r") as outf:
-        for line_exp, line_out in zip(expf, outf):
-            assert line_exp == line_out
-    os.remove(os.path.join(lst_dir, name + ".lst"))
-    os.remove(os.path.join(lst_dir, name + ".prt"))
-    os.remove(os.path.join(lst_dir, name + ".fna"))
-    os.remove(os.path.join(lst_dir, name + ".gen"))
-    os.remove(os.path.join(lst_dir, name + ".gff"))
-
-
-def test_format1genome_change_head():
-    """
-    Test that formatting a genome (making .prt, .gen, .fna, .lst) works, with a genome
-    which changed its name between prokka and format step.
-    """
-    ginit = os.path.join("test", "data", "annotate", "genomes", "B2_A3_5.fasta-changeName.fna")
-    gpath = os.path.join("test", "data", "annotate", "genomes",
-                         "B2_A3_5.fasta-changeName.fna-short-contig.fna")
-    shutil.copyfile(ginit, gpath)
-    name = "test.0417.00002"
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    lst_dir = os.path.join("test", "data", "annotate")
-    prot_dir = lst_dir
-    gene_dir = lst_dir
-    rep_dir = lst_dir
-    gff_dir = lst_dir
-    assert ffunc.format_one_genome(gpath, name, prok_path, lst_dir,
-                                   prot_dir, gene_dir, rep_dir, gff_dir, my_logger()[1])
-    # Check that all files were created
-    assert os.path.isfile(os.path.join(lst_dir, name + ".lst"))
-    assert os.path.isfile(os.path.join(lst_dir, name + ".fna"))
-    assert os.path.isfile(os.path.join(lst_dir, name + ".prt"))
-    assert os.path.isfile(os.path.join(lst_dir, name + ".gen"))
-    assert os.path.isfile(os.path.join(lst_dir, name + ".gff"))
-    # Check the contents of the files
-    explst = os.path.join(prok_path, "res_format-B2.lst")
-    expprt = os.path.join(prok_path, "res_format-B2.prt")
-    expgen = os.path.join(prok_path, "res_format-B2.gen")
-    expgff = os.path.join(prok_path, "res_format-B2.gff")
-    expreplicons = os.path.join("test", "data", "annotate", "genomes",
-                                "B2_A3_5.fasta-split5N.fna-short-contig.fna")
-    with open(explst, "r") as lstf, open(os.path.join(lst_dir, name + ".lst"), "r") as lsto:
-        for line_exp, line_out in zip(lstf, lsto):
-            assert line_exp == line_out
-    with open(expprt, "r") as expf, open(os.path.join(lst_dir, name + ".prt"), "r") as outf:
-        for line_exp, line_out in zip(expf, outf):
-            assert line_exp == line_out
-    with open(expgen, "r") as expf, open(os.path.join(lst_dir, name + ".gen"), "r") as outf:
-        for line_exp, line_out in zip(expf, outf):
-            assert line_exp == line_out
-    with open(expgff, "r") as expf, open(os.path.join(lst_dir, name + ".gff"), "r") as outf:
-        for line_exp, line_out in zip(expf, outf):
-            assert line_exp == line_out
-    with open(expreplicons, "r") as expf, open(os.path.join(lst_dir, name + ".fna"), "r") as outf:
-        for line_exp, line_out in zip(expf, outf):
-            assert line_exp == line_out
-    os.remove(os.path.join(lst_dir, name + ".lst"))
-    os.remove(os.path.join(lst_dir, name + ".prt"))
-    os.remove(os.path.join(lst_dir, name + ".fna"))
-    os.remove(os.path.join(lst_dir, name + ".gen"))
-    os.remove(os.path.join(lst_dir, name + ".gff"))
-    os.remove(gpath)
 
-
-def test_format1genome_problemgen():
-    """
-    Test that formatting a genome (making .prt, .gen, .fna, .lst) returns an error message
-    and does not create any output file if there is a problem while converting the
-    .ffn to .gen
-    """
-    logger = my_logger()
-    gpath = os.path.join("test", "data", "annotate", "genomes",
-                         "B2_A3_5.fasta-problems.fna-short-contig.fna")
-    name = "test.0417.00002"
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".tbl")
-    tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".tbl")
-    shutil.copyfile(tbl_init, tblout)
-    gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".gff")
-    gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".gff")
-    shutil.copyfile(gff_init, gffout)
-    lst_dir = os.path.join("test", "data", "annotate")
-    prot_dir = lst_dir
-    gene_dir = lst_dir
-    rep_dir = lst_dir
-    gff_dir = lst_dir
-    assert not ffunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir,
-                                       gene_dir, rep_dir, gff_dir, logger[1])
-    # Check that all files were not created
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".lst"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".fna"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".prt"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".gen"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".gff"))
-    msg = ("Unknown header format >EPKOMDHM_i00002 hypothetical protein in "
-           "test/data/annotate/exp_files/B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes/"
-           "test.0417.00002.ffn.\n"
-           "Gen file will not be created.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-    # remove tblout which was copied for this test
-    os.remove(tblout)
-    os.remove(gffout)
-
-
-def test_format1genome_problemprt():
-    """
-    Test that formatting a genome (making .prt, .gen, .fna, .lst) works, with a genome
-    which did not change name between prokka run and format step.
-    """
-    logger = my_logger()
-    gpath = os.path.join("test", "data", "annotate", "genomes",
-                         "B2_A3_5.fasta-problems.fna-short-contig.fna")
-    name = "test.0417.00002"
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    # copy tbl without errors to error prokka dir
-    tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".tbl")
-    tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".tbl")
-    shutil.copyfile(tbl_init, tblout)
-    # copy gff without errors to error prokka dir
-    gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".gff")
-    gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".gff")
-    shutil.copyfile(gff_init, gffout)
-    # copy ffn without error to error prokka dir
-    ffn_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".ffn")
-    ffn_ok = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".ffn")
-    ffn_error = ffn_ok + "-error"
-    # change name of ffn file with error to keep it for later (used for tests)
-    shutil.copyfile(ffn_ok, ffn_error)
-    # copy ffn without error to prokka res (erasing ffn with error)
-    shutil.copyfile(ffn_init, ffn_ok)
-    lst_dir = os.path.join("test", "data", "annotate")
-    prot_dir = lst_dir
-    gene_dir = lst_dir
-    rep_dir = lst_dir
-    gff_dir = lst_dir
-    assert not ffunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir,
-                                       gene_dir, rep_dir, gff_dir, logger[1])
-    # Check that all files were not created
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".lst"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".fna"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".prt"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".gen"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".gff"))
-    msg = ("Unknown header format >EPKOMDHM00003 hypothetical protein in "
-           "test/data/annotate/exp_files/B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes/"
-           "test.0417.00002.faa. "
-           "Error: invalid literal for int() with base 10: '>EPKOMDHM00003'\n"
-           "Prt file not created from test/data/annotate/exp_files/"
-           "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes/test.0417.00002.faa.")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-    # remove files which were copied for this test (tblout). And rename ffn with errors
-    # to its original name.
-    os.rename(ffn_error, ffn_ok)
-    os.remove(tblout)
-    os.remove(gffout)
-
-
-def test_format1genome_problemgff():
-    """
-    Test that formatting a genome (making .prt, .gen, .fna, .lst) returns an error message
-    and does not create any output file if there is a problem while converting the
-    .ffn to .gen
-    """
-    logger = my_logger()
-    gpath = os.path.join("test", "data", "annotate", "genomes",
-                         "B2_A3_5.fasta-problems.fna-short-contig.fna")
-    name = "test.0417.00002"
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".tbl")
-    tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".tbl")
-    shutil.copyfile(tbl_init, tblout)
-    gff_init = os.path.join("test", "data", "annotate", "test_files", "prokka_out_gff-error.gff")
-    gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".gff")
-    shutil.copyfile(gff_init, gffout)
-    lst_dir = os.path.join("test", "data", "annotate")
-    prot_dir = lst_dir
-    gene_dir = lst_dir
-    rep_dir = lst_dir
-    gff_dir = lst_dir
-    assert not ffunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir,
-                                       gene_dir, rep_dir, gff_dir, logger[1])
-    # Check that all files were not created
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".lst"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".fna"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".prt"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".gen"))
-    assert not os.path.isfile(os.path.join(lst_dir, name + ".gff"))
-    msg = ("Problem with your gff file. '##FASTA' is not a gff entry line, whereas it should "
-           "correspond to '11249\t12328\tD\tCDS\ttest.0417.00002.i0002_00016\tNA\t"
-           "| hypothetical protein | NA | NA'")
-    q = logger[0]
-    assert q.qsize() == 1
-    assert q.get().message == msg
-    # remove tblout which was copied for this test
-    os.remove(tblout)
-    os.remove(gffout)
-
-
-def test_format_all():
-    """
-    Test that when giving a list of genomes, for which prokka ran without problem,
-    they are formatted, with all expected files created.
-    """
-    # genomes = {genome: [name, gpath, size, nbcont, l90]}
-    initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
-    initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
-    gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
-    onames = ["test_runprokka_H299", "test.0417.00002"]
-    gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
-    for f1, f2 in zip(initpaths, gpaths):
-        shutil.copyfile(f1, f2)
-    genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
-               gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
-               }
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    res_path = os.path.join("test", "data", "annotate")
-    results = {gname: True for gname in gnames}
-    skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path,
-                                                   prok_path, threads=4)
-    assert skipped == []
-    assert skipped_format == []
-    lstfiles = [os.path.join(res_path, "LSTINFO", name + ".lst") for name in onames]
-    prtfiles = [os.path.join(res_path, "Proteins", name + ".prt") for name in onames]
-    genfiles = [os.path.join(res_path, "Genes", name + ".gen") for name in onames]
-    repfiles = [os.path.join(res_path, "Replicons", name + ".fna") for name in onames]
-    gfffiles = [os.path.join(res_path, "gff3", name + ".gff") for name in onames]
-    for f in lstfiles + prtfiles + genfiles + repfiles + gfffiles:
-        assert os.path.isfile(f)
-    shutil.rmtree(os.path.join(res_path, "LSTINFO"))
-    shutil.rmtree(os.path.join(res_path, "Proteins"))
-    shutil.rmtree(os.path.join(res_path, "Genes"))
-    shutil.rmtree(os.path.join(res_path, "Replicons"))
-    shutil.rmtree(os.path.join(res_path, "gff3"))
-    for f in gpaths:
-        os.remove(f)
-
-
-def test_format_all_result_false():
-    """
-    Test that when giving a list of 2 genomes, 1 for which prokka ran without problem,
-    1 for which prokka had problems (given with False in results),
-    the correct genome is formatted, with all
-    expected files created, and the genome with problems is not formatted.
-    """
-    # genomes = {genome: [name, gpath, size, nbcont, l90]}
-    initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
-    initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
-    gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
-    onames = ["test_runprokka_H299", "test.0417.00002"]
-    gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
-    for f1, f2 in zip(initpaths, gpaths):
-        shutil.copyfile(f1, f2)
-    genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
-               gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
-               }
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    res_path = os.path.join("test", "data", "annotate")
-    results = {gnames[0]: True, gnames[1]: False}
-    skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
-    assert skipped == ["B2_A3_5.fasta-changeName.fna-short-contig.fna"]
-    assert skipped_format == []
-    lstfiles = os.path.join(res_path, "LSTINFO")
-    prtfiles = os.path.join(res_path, "Proteins")
-    genfiles = os.path.join(res_path, "Genes")
-    repfiles = os.path.join(res_path, "Replicons")
-    gfffiles = os.path.join(res_path, "gff3")
-    assert os.path.isfile(os.path.join(lstfiles, onames[0] + ".lst"))
-    assert not os.path.isfile(os.path.join(lstfiles, onames[1] + ".lst"))
-    assert os.path.isfile(os.path.join(prtfiles, onames[0] + ".prt"))
-    assert not os.path.isfile(os.path.join(prtfiles, onames[1] + ".prt"))
-    assert os.path.isfile(os.path.join(genfiles, onames[0] + ".gen"))
-    assert not os.path.isfile(os.path.join(genfiles, onames[1] + ".gen"))
-    assert os.path.isfile(os.path.join(repfiles, onames[0] + ".fna"))
-    assert not os.path.isfile(os.path.join(repfiles, onames[1] + ".fna"))
-    assert os.path.isfile(os.path.join(gfffiles, onames[0] + ".gff"))
-    assert not os.path.isfile(os.path.join(gfffiles, onames[1] + ".gff"))
-    shutil.rmtree(os.path.join(res_path, "LSTINFO"))
-    shutil.rmtree(os.path.join(res_path, "Proteins"))
-    shutil.rmtree(os.path.join(res_path, "Genes"))
-    shutil.rmtree(os.path.join(res_path, "Replicons"))
-    shutil.rmtree(os.path.join(res_path, "gff3"))
-    for f in gpaths:
-        os.remove(f)
-
-
-def test_format_all_not_result():
-    """
-    Test that when giving a list of 2 genomes, but only 1 is in the results list (and prokka ran
-    without problems for it), the correct genome is formatted, with all
-    expected files created, and the other genome is not formatted, and does not appear in
-    skipped list (as it was removed from the study before annotation step, probably by QC).
-    """
-    # genomes = {genome: [name, gpath, size, nbcont, l90]}
-    initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
-    initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
-    gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
-    onames = ["test_runprokka_H299", "test.0417.00002"]
-    gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
-    for f1, f2 in zip(initpaths, gpaths):
-        shutil.copyfile(f1, f2)
-    genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
-               gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
-               }
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    res_path = os.path.join("test", "data", "annotate")
-    results = {gnames[0]: True}
-    skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
-    assert skipped == []
-    assert skipped_format == []
-    lstfiles = os.path.join(res_path, "LSTINFO")
-    prtfiles = os.path.join(res_path, "Proteins")
-    genfiles = os.path.join(res_path, "Genes")
-    repfiles = os.path.join(res_path, "Replicons")
-    gfffiles = os.path.join(res_path, "gff3")
-    assert os.path.isfile(os.path.join(lstfiles, onames[0] + ".lst"))
-    assert not os.path.isfile(os.path.join(lstfiles, onames[1] + ".lst"))
-    assert os.path.isfile(os.path.join(prtfiles, onames[0] + ".prt"))
-    assert not os.path.isfile(os.path.join(prtfiles, onames[1] + ".prt"))
-    assert os.path.isfile(os.path.join(genfiles, onames[0] + ".gen"))
-    assert not os.path.isfile(os.path.join(genfiles, onames[1] + ".gen"))
-    assert os.path.isfile(os.path.join(repfiles, onames[0] + ".fna"))
-    assert not os.path.isfile(os.path.join(repfiles, onames[1] + ".fna"))
-    assert os.path.isfile(os.path.join(gfffiles, onames[0] + ".gff"))
-    assert not os.path.isfile(os.path.join(gfffiles, onames[1] + ".gff"))
-    shutil.rmtree(os.path.join(res_path, "LSTINFO"))
-    shutil.rmtree(os.path.join(res_path, "Proteins"))
-    shutil.rmtree(os.path.join(res_path, "Genes"))
-    shutil.rmtree(os.path.join(res_path, "Replicons"))
-    shutil.rmtree(os.path.join(res_path, "gff3"))
-    for f in gpaths:
-        os.remove(f)
-
-        # probleme avec .fna de onames[0] qui n'est pas créé...
-
-
-def test_format_all_error():
-    """
-    Test that when giving a list of 2 genomes, prokka ran without problem for both.
-    But a problem appears while formatting the 2nd one. So, the 2nd one is not formatted,
-    and appears in skipped_format. The first one is formated, and check that all
-    output files are created.
-    """
-    # genomes = {genome: [name, gpath, size, nbcont, l90]}
-    name = "test.0417.00002"
-    initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
-    initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
-    gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-problems.fna-short-contig.fna"]
-    onames = ["test_runprokka_H299", "test.0417.00002"]
-    gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
-    for f1, f2 in zip(initpaths, gpaths):
-        shutil.copyfile(f1, f2)
-    genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
-               gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
-               }
-    prok_path = os.path.join("test", "data", "annotate", "exp_files")
-    res_path = os.path.join("test", "data", "annotate")
-    tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".tbl")
-    tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".tbl")
-    shutil.copyfile(tbl_init, tblout)
-    gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
-                            name + ".gff")
-    gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
-                          name + ".gff")
-    shutil.copyfile(gff_init, gffout)
-    results = {gnames[0]: True, gnames[1]: True}
-    skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
-    assert skipped == []
-    assert skipped_format == ["B2_A3_5.fasta-problems.fna-short-contig.fna"]
-    lstfiles = os.path.join(res_path, "LSTINFO")
-    prtfiles = os.path.join(res_path, "Proteins")
-    genfiles = os.path.join(res_path, "Genes")
-    repfiles = os.path.join(res_path, "Replicons")
-    gfffiles = os.path.join(res_path, "gff3")
-    assert os.path.isfile(os.path.join(lstfiles, onames[0] + ".lst"))
-    assert not os.path.isfile(os.path.join(lstfiles, onames[1] + ".lst"))
-    assert os.path.isfile(os.path.join(prtfiles, onames[0] + ".prt"))
-    assert not os.path.isfile(os.path.join(prtfiles, onames[1] + ".prt"))
-    assert os.path.isfile(os.path.join(genfiles, onames[0] + ".gen"))
-    assert not os.path.isfile(os.path.join(genfiles, onames[1] + ".gen"))
-    assert os.path.isfile(os.path.join(repfiles, onames[0] + ".fna"))
-    assert not os.path.isfile(os.path.join(repfiles, onames[1] + ".fna"))
-    assert os.path.isfile(os.path.join(gfffiles, onames[0] + ".gff"))
-    assert not os.path.isfile(os.path.join(gfffiles, onames[1] + ".gff"))
-    shutil.rmtree(os.path.join(res_path, "LSTINFO"))
-    shutil.rmtree(os.path.join(res_path, "Proteins"))
-    shutil.rmtree(os.path.join(res_path, "Genes"))
-    shutil.rmtree(os.path.join(res_path, "Replicons"))
-    shutil.rmtree(os.path.join(res_path, "gff3"))
-    os.remove(tblout)
-    os.remove(gffout)
-    for f in gpaths:
-        os.remove(f)
+# def test_tbl_to_lst_new_name():
+#     """
+#     Check that generated lstinfo file is as expected, when the genome name has changed between
+#     the one given to prokka, and the name given now.
+#     The test tblfile contains the following aspects:
+#     - gene in D strand (start < end)
+#     - gene in C strand (start > end)
+#     - CDS features (some with all info = ECnumber, gene name, product etc. ;
+#     some with missing info)
+#     - tRNA type
+#     - repeat_region type (*2)
+#     - contigs with more than 2 genes
+#     - contig with only 2 genes (both 'b' loc)
+#     - contig with 1 gene ('b' loc)
+#     - contig without gene (should be skipped)
+#     """
+#     tblfile = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
+#                            "prokka_out_for_test.tbl")
+#     lstfile = os.path.join("test", "data", "annotate", "test_tbl2lstNewName.lst")
+#     exp_lst = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst-newName.lst")
+#     name = "test.0417.00010"
+#     assert not ffunc.tbl2lst(tblfile, lstfile, name)
+#     with open(exp_lst, "r") as expf, open(lstfile, "r") as lstf:
+#         for line_exp, line_out in zip(expf, lstf):
+#             assert line_exp == line_out
+#     os.remove(lstfile)
+
+
+# def test_write_header_gene():
+#     """
+#     From a given line of lstinfo file, giving info for a gene (start, end, gene name,
+#     product, EC number, more information), check that the header line of the protein and
+#     gene files are generated as expected.
+#     """
+#     outfile = StringIO()
+#     lstline = ("4416\t6068\tD\tCDS\ttest.0417.00002.i0001_00005\tyiaD\t| "
+#                "putative lipoprotein YiaD | 6.3.2.- | similar to AA sequence:UniProtKB:P37665")
+#     ffunc.write_header(lstline, outfile)
+#     res = outfile.getvalue()
+#     exp = (">test.0417.00002.i0001_00005 1653 yiaD | putative lipoprotein YiaD | 6.3.2.- "
+#            "| similar to AA sequence:UniProtKB:P37665\n")
+#     assert res == exp
+#     outfile.close()
+
+
+# def test_write_header_gene_no_name():
+#     """
+#     From a given line of lstinfo file, giving info for a gene with many unknown parts (gene
+#     name, product, EC number and more information are NAs), check that the header line of the
+#     protein and gene files are generated as expected.
+#     """
+#     outfile = StringIO()
+#     lstline = ("4632\t5000\tC\tCDS\ttest.0417.00002.b0002_00011\tNA\t| hypothetical protein "
+#                "| NA | NA")
+#     ffunc.write_header(lstline, outfile)
+#     res = outfile.getvalue()
+#     exp = ">test.0417.00002.b0002_00011 369 NA | hypothetical protein | NA | NA\n"
+#     assert res == exp
+#     outfile.close()
+
+
+# def test_write_header_crispr():
+#     """
+#     From a given line of lstinfo file, giving info for a CRISPR check that the header
+#     line of the protein and gene files are generated as expected.
+#     """
+#     outfile = StringIO()
+#     lstline = ("296902\t2968265\tC\tCRISPR\ttest.0417.00002.b0003_CRISPR1\tcrispr\t| "
+#                "crispr-array | NA | NA")
+#     ffunc.write_header(lstline, outfile)
+#     res = outfile.getvalue()
+#     exp = ">test.0417.00002.b0003_CRISPR1 2671364 crispr | crispr-array | NA | NA\n"
+#     assert res == exp
+#     outfile.close()
+
+
+# def test_create_prt_wrong_header_sep():
+#     """
+#     Test that, when creating prt file from faa and lst, if a header of faa file is
+#     not in the right format (protein name and number are not separated by '_'),
+#     it writes an error, erases prt file, and returns False.
+#     """
+#     logger = my_logger()
+#     faaseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-wrongHeaderSep.faa")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     prtseq = os.path.join("test", "data", "annotate", "test_create_prt-wrongHeadSep.prt")
+#     assert not ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
+#     assert not os.path.isfile(prtseq)
+#     msg = ("Unknown header format >JGIKIPIJ00008 in test/data/annotate/test_files/"
+#            "prokka_out_for_test-wrongHeaderSep.faa. Error: invalid literal for int() "
+#            "with base 10: '>JGIKIPIJ00008'\nPrt file not created from "
+#            "test/data/annotate/test_files/prokka_out_for_test-wrongHeaderSep.faa.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_prt_wrong_header_int():
+#     """
+#     Test that, when creating prt file from faa and lst, if a header of faa file is
+#     not in the right format (protein name and number are separated by '_', but protein num
+#     contains a letter), it writes an error, erases prt file, and returns False.
+#     """
+#     logger = my_logger()
+#     faaseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-wrongHeaderInt.faa")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     prtseq = os.path.join("test", "data", "annotate", "test_create_prt-wrongHeadInt.prt")
+#     assert not ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
+#     assert not os.path.isfile(prtseq)
+#     msg = ("Unknown header format >JGIKIPIJ_d0008 in test/data/annotate/test_files/"
+#            "prokka_out_for_test-wrongHeaderInt.faa. Error: invalid literal for int() "
+#            "with base 10: 'd0008'\nPrt file not created from "
+#            "test/data/annotate/test_files/prokka_out_for_test-wrongHeaderInt.faa.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_prt_miss_lst():
+#     """
+#     Test that, when creating prt file from faa and lst, if a protein of faa file is not present in
+#     the lst file, it writes an error, removes the prt file, and returns False.
+#     """
+#     logger = my_logger()
+#     faaseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-supHeader.faa")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     prtseq = os.path.join("test", "data", "annotate", "test_create_prt-missLst.prt")
+#     assert not ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
+#     assert not os.path.isfile(prtseq)
+#     msg = ("Missing info for protein >sup-prot_00012 in "
+#            "test/data/annotate/exp_files/res_tbl2lst.lst. If it is "
+#            "actually present in the lst file, check that proteins are ordered by "
+#            "increasing number in both lst and faa files.\n"
+#            "Prt file not created from test/data/annotate/test_files/"
+#            "prokka_out_for_test-supHeader.faa.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_prt_wrong_order():
+#     """
+#     Test that, when creating prt file from faa and lst, if a protein of faa file is not in
+#     increasing protein number, so that it does not correspond to the protein in the lstinfo file,
+#     it writes an error, removes the prt file, and returns False.
+#     """
+#     logger = my_logger()
+#     faaseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-wrongOrder.faa")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     prtseq = os.path.join("test", "data", "annotate", "test_create_prt-wrongOrder.prt")
+#     assert not ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
+#     assert not os.path.isfile(prtseq)
+#     msg = ("Missing info for protein >appears_after_13_00011 in "
+#            "test/data/annotate/exp_files/res_tbl2lst.lst. If it is "
+#            "actually present in the lst file, check that proteins are ordered by "
+#            "increasing number in both lst and faa files.\n"
+#            "Prt file not created from test/data/annotate/test_files/"
+#            "prokka_out_for_test-wrongOrder.faa.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_prt_ok():
+#     """
+#     Test that when everything is ok in both faa and lst files, the prt file is
+#     created as expected.
+#     """
+#     logger = my_logger()
+#     faaseq = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
+#                           "prokka_out_for_test.faa")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     prtseq = os.path.join("test", "data", "annotate", "test_create_prt.prt")
+#     assert ffunc.create_prt(faaseq, lstfile, prtseq, logger[1])
+#     exp_file = os.path.join("test", "data", "annotate", "exp_files", "res_create_prt.faa")
+#     with open(exp_file, "r") as expf, open(prtseq, "r") as prtf:
+#         for line_exp, line_out in zip(expf, prtf):
+#             assert line_exp == line_out
+#     os.remove(prtseq)
+
+
+# def test_create_gen_sup_crispr():
+#     """
+#     Test that when there is a CRISPR in the ffn file, but not in lstinfo,
+#     it generates an error, because the CRISPR ID does not correspond to the gene ID in lstinfo.
+#     It should return False, write an error message, and remove the .gen file.
+#     Moreover, the CRISPR ID is not in the same format as a gene ID, so the error should
+#     be on the format.
+#     """
+#     logger = my_logger()
+#     ffnseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-supCRISPR.ffn")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     genseq = os.path.join("test", "data", "annotate", "test_create_gen_supCRISPR.gen")
+#     assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
+#     assert not os.path.isfile(genseq)
+#     msg = ("Unknown header format >prokka_out_for_test in test/data/annotate/test_files/"
+#            "prokka_out_for_test-supCRISPR.ffn.\nGen file will not be created.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_gen_sup_gene():
+#     """
+#     Test that, when creating gen file from ffn and lst, if a gene of ffn file is not present in
+#     the lst file, it writes an error, removes the gen file, and returns False.
+#     """
+#     logger = my_logger()
+#     ffnseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-supGene.ffn")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     prtseq = os.path.join("test", "data", "annotate", "test_create_gen-supgene.prt")
+#     assert not ffunc.create_gen(ffnseq, lstfile, prtseq, logger[1])
+#     assert not os.path.isfile(prtseq)
+#     msg = ("Missing info for gene >sup_gene_00012 in test/data/annotate/exp_files/"
+#            "res_tbl2lst.lst. If it is actually present "
+#            "in the lst file, check that genes are ordered by increasing "
+#            "number in both lst and ffn files.\nGen file not created"
+#            " from test/data/annotate/test_files/prokka_out_for_test-supGene.ffn.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_gen_miss_crispr():
+#     """
+#     Test for situation where there are 2 CRISPRs in the lstinfo file, the first one
+#     is not in the ffn file, while the second one is in the ffn file.
+#     It should return an error message about CRISPR number not corresponding, as
+#     the first CRISPR found in ffn (CRISPR 1) corresponds to CRISPR2 in lstinfo file.
+#     Gene file should be removed, and the function should return False
+#     """
+#     logger = my_logger()
+#     ffnseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-missCRISPR.ffn")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     genseq = os.path.join("test", "data", "annotate", "test_create_gen_missCRISPR.gen")
+#     assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
+#     assert not os.path.isfile(genseq)
+#     msg = ("Problem with CRISPR numbers in test/data/annotate/exp_files/res_tbl2lst.lst. "
+#            "CRISPR >prokka_out_for_test in ffn is CRISPR num 1, whereas it is annotated "
+#            "as CRISPR num 2 in lst file.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_gen_no_crispr_ffn():
+#     """
+#     Test that when the there is a CRISPR in the lst file, but not in the ffn file,
+#     everything goes well, as in some versions of prokka (1.12)n CRISPRs are not in ffn while
+#     they are specified in lst. Function should return True, and gene file created.
+#     """
+#     ffnseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-noCRISPRffn.ffn")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     genseq = os.path.join("test", "data", "annotate", "test_create_gen_noCRISPRffn.gen")
+#     assert ffunc.create_gen(ffnseq, lstfile, genseq, my_logger()[1])
+#     assert os.path.isfile(genseq)
+#     exp_file = os.path.join("test", "data", "annotate", "exp_files",
+#                             "res_create_gen_noCRISPRffn.gen")
+#     with open(exp_file, "r") as expf, open(genseq, "r") as prtf:
+#         for line_exp, line_out in zip(expf, prtf):
+#             assert line_exp == line_out
+#     os.remove(genseq)
+
+
+# def test_create_gen_wrong_header_sep():
+#     """
+#     Test that, when creating gen file from ffn and lst, if a header of ffn file is
+#     not in the right format (gene name and number are not separated by '_'),
+#     it writes an error, erases gen file, and returns False.
+#     """
+#     logger = my_logger()
+#     ffnseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-wrongFormat.ffn")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     genseq = os.path.join("test", "data", "annotate", "test_create_gen_wrongHeadSep.gen")
+#     assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
+#     assert not os.path.isfile(genseq)
+#     msg = ("Unknown header format >JGIKIPIJ-00005 in test/data/annotate/test_files/"
+#            "prokka_out_for_test-wrongFormat.ffn.\n"
+#            "Gen file will not be created.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_gen_wrong_header_int():
+#     """
+#     Test that, when creating gen file from ffn and lst, if a header of ffn file is
+#     not in the right format (gene name and number are separated by '_', but gene num
+#     contains a letter), it writes an error, erases gen file, and returns False.
+#     """
+#     logger = my_logger()
+#     ffnseq = os.path.join("test", "data", "annotate", "test_files",
+#                           "prokka_out_for_test-wrongInt.ffn")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     genseq = os.path.join("test", "data", "annotate", "test_create_gen_wrongHeadInt.gen")
+#     assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
+#     assert not os.path.isfile(genseq)
+#     msg = ("Unknown header format >JGIKIPIJ_a00005 in test/data/annotate/test_files/"
+#            "prokka_out_for_test-wrongInt.ffn.\n"
+#            "Gen file will not be created.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_gen_wrong_lst_int():
+#     """
+#     Test that, when creating gen file from ffn and lst, if a gene name in lst file is
+#     not in the right format (gene name and number are separated by '_', but gene num
+#     contains a letter), it writes an error, erases gen file, and returns False.
+#     Because the gene name in ffn won't be found in lst (a it contains an error in lst).
+#     """
+#     logger = my_logger()
+#     ffnseq = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
+#                           "prokka_out_for_test.ffn")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst-wrongGeneName.lst")
+#     genseq = os.path.join("test", "data", "annotate", "test_create_gen_wrongLstHeadInt.gen")
+#     assert not ffunc.create_gen(ffnseq, lstfile, genseq, logger[1])
+#     assert not os.path.isfile(genseq)
+#     msg = ("Missing info for gene >JGIKIPIJ_00009 in test/data/annotate/exp_files/"
+#            "res_tbl2lst-wrongGeneName.lst. If it is actually present "
+#            "in the lst file, check that genes are ordered by increasing "
+#            "number in both lst and ffn files.\nGen file not created "
+#            "from test/data/annotate/test_files/original_name.fna-prokkaRes/"
+#            "prokka_out_for_test.ffn.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+
+
+# def test_create_gen_ok():
+#     """
+#     Test that when everything is ok in both ffn and lst files, the gen file is
+#     created as expected.
+#     """
+#     faaseq = os.path.join("test", "data", "annotate", "test_files", "original_name.fna-prokkaRes",
+#                           "prokka_out_for_test.ffn")
+#     lstfile = os.path.join("test", "data", "annotate", "exp_files", "res_tbl2lst.lst")
+#     genseq = os.path.join("test", "data", "annotate", "test_create_gen.gen")
+#     assert ffunc.create_gen(faaseq, lstfile, genseq, my_logger()[1])
+#     exp_file = os.path.join("test", "data", "annotate", "exp_files", "res_create_gen.gen")
+#     with open(exp_file, "r") as expf, open(genseq, "r") as prtf:
+#         for line_exp, line_out in zip(expf, prtf):
+#             assert line_exp == line_out
+#     os.remove(genseq)
+
+
+# def test_handle_line_gff():
+#     """
+#     Check that given a line in lstinfo with no information (gene name, ecnumber, product,
+#     inference), it returns the good gff line
+#     """
+#     line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tNA\t"
+#                 "| NA | NA | NA")
+#     line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
+#                 "ID=ONKACNIE_00001;inference=ab initio "
+#                 "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
+#     outgff = "test_handle_line_gff.gff"
+#     gfff = open(outgff, "w")
+#     ffunc.handle_line_gff(line_lst, line_gff, gfff)
+#     gfff.close()
+#     with open(outgff, "r") as gf:
+#         lines = gf.readlines()
+#         assert len(lines) == 1
+#         exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
+#                     "ID=ESCO.1015.00001.b0001_00001;locus_tag=ESCO.1015.00001.b0001_00001\n")
+#         assert lines[0] == exp_line
+#     os.remove(outgff)
+
+
+# def test_handle_line_gff_ecnum():
+#     """
+#     Check that given a line in lstinfo with only ec_number information,
+#     it returns the good gff line
+#     """
+#     line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tNA\t"
+#                 "| NA | 123.995.4546 | NA")
+#     line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
+#                 "ID=ONKACNIE_00001;inference=ab initio "
+#                 "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
+#     outgff = "test_handle_line_gff-ecnum.gff"
+#     gfff = open(outgff, "w")
+#     ffunc.handle_line_gff(line_lst, line_gff, gfff)
+#     gfff.close()
+#     with open(outgff, "r") as gf:
+#         lines = gf.readlines()
+#         assert len(lines) == 1
+#         exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
+#                     "ID=ESCO.1015.00001.b0001_00001;eC_number=123.995.4546;"
+#                     "locus_tag=ESCO.1015.00001.b0001_00001\n")
+#         assert lines[0] == exp_line
+#     os.remove(outgff)
+
+
+# def test_handle_line_gff_gene():
+#     """
+#     Check that given a line in lstinfo with only gene name information,
+#     it returns the good gff line
+#     """
+#     line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tge4a\t"
+#                 "| NA | NA | NA")
+#     line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
+#                 "ID=ONKACNIE_00001;inference=ab initio "
+#                 "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
+#     outgff = "test_handle_line_gff-gene.gff"
+#     gfff = open(outgff, "w")
+#     ffunc.handle_line_gff(line_lst, line_gff, gfff)
+#     gfff.close()
+#     with open(outgff, "r") as gf:
+#         lines = gf.readlines()
+#         assert len(lines) == 1
+#         exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
+#                     "ID=ESCO.1015.00001.b0001_00001;Name=ge4a;gene=ge4a;"
+#                     "locus_tag=ESCO.1015.00001.b0001_00001\n")
+#         assert lines[0] == exp_line
+#     os.remove(outgff)
+
+
+# def test_handle_line_gff_inf():
+#     """
+#     Check that given a line in lstinfo with only inference information,
+#     it returns the good gff line
+#     """
+#     line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tNA\t"
+#                 "| NA | NA | ab initio prediction:Prodigal:2.6")
+#     line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
+#                 "ID=ONKACNIE_00001;inference=ab initio "
+#                 "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
+#     outgff = "test_handle_line_gff-inf.gff"
+#     gfff = open(outgff, "w")
+#     ffunc.handle_line_gff(line_lst, line_gff, gfff)
+#     gfff.close()
+#     with open(outgff, "r") as gf:
+#         lines = gf.readlines()
+#         assert len(lines) == 1
+#         exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
+#                     "ID=ESCO.1015.00001.b0001_00001;inference=ab initio "
+#                     "prediction:Prodigal:2.6;locus_tag=ESCO.1015.00001.b0001_00001\n")
+#         assert lines[0] == exp_line
+#     os.remove(outgff)
+
+
+# def test_handle_line_gff_prod():
+#     """
+#     Check that given a line in lstinfo with only product information,
+#     it returns the good gff line
+#     """
+#     line_lst = ("201\t743\tC\tCDS\tESCO.1015.00001.b0001_00001\tNA\t"
+#                 "| hypothetical protein | NA | NA")
+#     line_gff = ("H561_S27_L001__1\tProdigal:2.6\tCDS\t201\t743\t.\t-\t0\t"
+#                 "ID=ONKACNIE_00001;inference=ab initio "
+#                 "prediction:Prodigal:2.6;locus_tag=ONKACNIE_00001;product=hypothetical protein")
+#     outgff = "test_handle_line_gff-prod.gff"
+#     gfff = open(outgff, "w")
+#     ffunc.handle_line_gff(line_lst, line_gff, gfff)
+#     gfff.close()
+#     with open(outgff, "r") as gf:
+#         lines = gf.readlines()
+#         assert len(lines) == 1
+#         exp_line = ("ESCO.1015.00001.0001\tProdigal:2.6\tCDS\t201\t743\t.\t-\t.\t"
+#                     "ID=ESCO.1015.00001.b0001_00001;locus_tag=ESCO.1015.00001.b0001_00001;"
+#                     "product=hypothetical protein\n")
+#         assert lines[0] == exp_line
+#     os.remove(outgff)
+
+
+# def test_generate_gff():
+#     """
+#     Test creating gff file.
+#     """
+#     prokgff = os.path.join("test", "data", "annotate", "test_files", "prokka_out_gff.gff")
+#     gffout = os.path.join("test", "data", "annotate", "test_creategff.gff")
+#     lstgenome = os.path.join("test", "data", "annotate", "test_files", "lstinfo_for_gff.lst")
+#     assert ffunc.generate_gff(prokgff, gffout, lstgenome, my_logger()[1])
+#     exp_gff = os.path.join("test", "data", "annotate", "exp_files", "res_create_gff.gff")
+#     with open(gffout, "r") as gffo, open(exp_gff, "r") as expf:
+#         for line_exp, line_out in zip(expf, gffo):
+#             assert line_exp == line_out
+#     os.remove(gffout)
+
+
+# def test_generate_gff_error():
+#     """
+#     Test creating gff file.
+#     """
+#     logger = my_logger()
+#     prokgff = os.path.join("test", "data", "annotate", "test_files", "prokka_out_gff-error.gff")
+#     lstgenome = os.path.join("test", "data", "annotate", "test_files", "lstinfo_for_gff.lst")
+#     gffout = os.path.join("test", "data", "annotate", "test_creategff.gff")
+#     assert not ffunc.generate_gff(prokgff, gffout, lstgenome, logger[1])
+#     os.remove(gffout)
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     logfound = q.get()
+#     msg = ("Problem with your gff file. '##FASTA' is not a gff entry line, whereas it should "
+#            "correspond to '863\t1795\tD\tCDS\tESCO.1015.00001.b0003_00016\tNA\t"
+#            "| hypothetical protein | NA | NA'")
+#     assert msg in logfound.message
+#     assert logfound.levelname == "ERROR"
+
+
+# def test_handle_genome_nores():
+#     """
+#     Test that when we try to format a genome which is not in results,
+#     it returns a tuple with "no_res" and the genome name.
+#     """
+#     results = {"abcd.fasta": True}
+#     args = ("toto.fasta", "name", "genome/path", "prokka/path", "lst/dir", "prot/dir",
+#             "gene/dir", "rep/dir", "gff/dir", results, my_logger()[0])
+#     res = ffunc.handle_genome(args)
+#     assert res == ("no_res", "toto.fasta")
+
+
+# def test_handle_genome_badprok():
+#     """
+#     Test that when we try to format a genome which is in results, but with False,
+#     it returns a tuple with "bad_prokka" and the genome name.
+#     """
+#     results = {"abcd.fasta": True, "toto.fasta": False}
+#     args = ("toto.fasta", "name", "genome/path", "prokka/path", "lst/dir", "prot/dir",
+#             "gene/dir", "rep/dir", "gff/dir", results, my_logger()[0])
+#     res = ffunc.handle_genome(args)
+#     assert res == ("bad_prokka", "toto.fasta")
+
+
+# def test_handle_genome_formatok():
+#     """
+#     Test that when we try to format a genome which is in results, with True,
+#     it returns a tuple with "True" and the genome name.
+#     """
+#     gpath = os.path.join("test", "data", "annotate", "genomes",
+#                          "B2_A3_5.fasta-split5N.fna-short-contig.fna")
+#     name = "test.0417.00002"
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     lst_dir = os.path.join("test", "data", "annotate")
+#     prot_dir = lst_dir
+#     gene_dir = lst_dir
+#     rep_dir = lst_dir
+#     gff_dir = lst_dir
+#     results = {"B2_A3_5.fasta-split5N.fna-short-contig.fna": True, "toto.fasta": False}
+#     args = ("B2_A3_5.fasta-split5N.fna-short-contig.fna", name, gpath, prok_path,
+#             lst_dir, prot_dir,
+#             gene_dir, rep_dir, gff_dir, results, my_logger()[0])
+#     res = ffunc.handle_genome(args)
+#     assert res == (True, "B2_A3_5.fasta-split5N.fna-short-contig.fna")
+#     os.remove(os.path.join(lst_dir, name + ".prt"))
+#     os.remove(os.path.join(lst_dir, name + ".fna"))
+#     os.remove(os.path.join(lst_dir, name + ".gen"))
+#     os.remove(os.path.join(lst_dir, name + ".lst"))
+#     os.remove(os.path.join(lst_dir, name + ".gff"))
+
+
+# def test_handle_genome_formaterror():
+#     """
+#     Test that when we try to format a genome which is in results, but with False,
+#     it returns a tuple with "bad_prokka" and the genome name.
+#     """
+#     logger = my_logger()
+#     gpath = os.path.join("test", "data", "annotate", "genomes",
+#                          "B2_A3_5.fasta-problems.fna-short-contig.fna")
+#     name = "test.0417.00002"
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".tbl")
+#     tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".tbl")
+#     shutil.copyfile(tbl_init, tblout)
+#     gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".gff")
+#     gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".gff")
+#     shutil.copyfile(gff_init, gffout)
+#     lst_dir = os.path.join("test", "data", "annotate")
+#     prot_dir = lst_dir
+#     gene_dir = lst_dir
+#     rep_dir = lst_dir
+#     gff_dir = lst_dir
+#     results = {"B2_A3_5.fasta-problems.fna-short-contig.fna": True, "toto.fasta": False}
+#     args = ("B2_A3_5.fasta-problems.fna-short-contig.fna", name, gpath,
+#             prok_path, lst_dir, prot_dir, gene_dir, rep_dir, gff_dir, results, logger[0])
+#     res = ffunc.handle_genome(args)
+#     assert res == (False, "B2_A3_5.fasta-problems.fna-short-contig.fna")
+#     msg = ("Unknown header format >EPKOMDHM_i00002 hypothetical protein in "
+#            "test/data/annotate/exp_files/B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes/"
+#            "test.0417.00002.ffn.\n"
+#            "Gen file will not be created.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+#     # remove tblout which was copied for this test
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".prt"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".gen"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".fna"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".lst"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".gff"))
+#     os.remove(tblout)
+#     os.remove(gffout)
+
+
+# def test_format1genome():
+#     """
+#     Test that formatting a genome (making .prt, .gen, .fna, .lst) works, with a genome
+#     which did not change name between prokka run and format step.
+#     """
+#     gpath = os.path.join("test", "data", "annotate", "genomes",
+#                          "B2_A3_5.fasta-split5N.fna-short-contig.fna")
+#     name = "test.0417.00002"
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     lst_dir = os.path.join("test", "data", "annotate")
+#     prot_dir = lst_dir
+#     gene_dir = lst_dir
+#     rep_dir = lst_dir
+#     gff_dir = lst_dir
+#     assert ffunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir,
+#                                    gene_dir, rep_dir, gff_dir, my_logger()[1])
+#     # Check that all files were created
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".lst"))
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".fna"))
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".prt"))
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".gen"))
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".gff"))
+#     # Check the contents of the files
+#     explst = os.path.join(prok_path, "res_format-B2.lst")
+#     expprt = os.path.join(prok_path, "res_format-B2.prt")
+#     expgen = os.path.join(prok_path, "res_format-B2.gen")
+#     expgff = os.path.join(prok_path, "res_format-B2.gff")
+#     with open(explst, "r") as lstf, open(os.path.join(lst_dir, name + ".lst"), "r") as lsto:
+#         for line_exp, line_out in zip(lstf, lsto):
+#             assert line_exp == line_out
+#     with open(expprt, "r") as expf, open(os.path.join(lst_dir, name + ".prt"), "r") as outf:
+#         for line_exp, line_out in zip(expf, outf):
+#             assert line_exp == line_out
+#     with open(expgen, "r") as expf, open(os.path.join(lst_dir, name + ".gen"), "r") as outf:
+#         for line_exp, line_out in zip(expf, outf):
+#             assert line_exp == line_out
+#     with open(gpath, "r") as expf, open(os.path.join(lst_dir, name + ".fna"), "r") as outf:
+#         for line_exp, line_out in zip(expf, outf):
+#             assert line_exp == line_out
+#     with open(expgff, "r") as expf, open(os.path.join(lst_dir, name + ".gff"), "r") as outf:
+#         for line_exp, line_out in zip(expf, outf):
+#             assert line_exp == line_out
+#     os.remove(os.path.join(lst_dir, name + ".lst"))
+#     os.remove(os.path.join(lst_dir, name + ".prt"))
+#     os.remove(os.path.join(lst_dir, name + ".fna"))
+#     os.remove(os.path.join(lst_dir, name + ".gen"))
+#     os.remove(os.path.join(lst_dir, name + ".gff"))
+
+
+# def test_format1genome_change_head():
+#     """
+#     Test that formatting a genome (making .prt, .gen, .fna, .lst) works, with a genome
+#     which changed its name between prokka and format step.
+#     """
+#     ginit = os.path.join("test", "data", "annotate", "genomes", "B2_A3_5.fasta-changeName.fna")
+#     gpath = os.path.join("test", "data", "annotate", "genomes",
+#                          "B2_A3_5.fasta-changeName.fna-short-contig.fna")
+#     shutil.copyfile(ginit, gpath)
+#     name = "test.0417.00002"
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     lst_dir = os.path.join("test", "data", "annotate")
+#     prot_dir = lst_dir
+#     gene_dir = lst_dir
+#     rep_dir = lst_dir
+#     gff_dir = lst_dir
+#     assert ffunc.format_one_genome(gpath, name, prok_path, lst_dir,
+#                                    prot_dir, gene_dir, rep_dir, gff_dir, my_logger()[1])
+#     # Check that all files were created
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".lst"))
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".fna"))
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".prt"))
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".gen"))
+#     assert os.path.isfile(os.path.join(lst_dir, name + ".gff"))
+#     # Check the contents of the files
+#     explst = os.path.join(prok_path, "res_format-B2.lst")
+#     expprt = os.path.join(prok_path, "res_format-B2.prt")
+#     expgen = os.path.join(prok_path, "res_format-B2.gen")
+#     expgff = os.path.join(prok_path, "res_format-B2.gff")
+#     expreplicons = os.path.join("test", "data", "annotate", "genomes",
+#                                 "B2_A3_5.fasta-split5N.fna-short-contig.fna")
+#     with open(explst, "r") as lstf, open(os.path.join(lst_dir, name + ".lst"), "r") as lsto:
+#         for line_exp, line_out in zip(lstf, lsto):
+#             assert line_exp == line_out
+#     with open(expprt, "r") as expf, open(os.path.join(lst_dir, name + ".prt"), "r") as outf:
+#         for line_exp, line_out in zip(expf, outf):
+#             assert line_exp == line_out
+#     with open(expgen, "r") as expf, open(os.path.join(lst_dir, name + ".gen"), "r") as outf:
+#         for line_exp, line_out in zip(expf, outf):
+#             assert line_exp == line_out
+#     with open(expgff, "r") as expf, open(os.path.join(lst_dir, name + ".gff"), "r") as outf:
+#         for line_exp, line_out in zip(expf, outf):
+#             assert line_exp == line_out
+#     with open(expreplicons, "r") as expf, open(os.path.join(lst_dir, name + ".fna"), "r") as outf:
+#         for line_exp, line_out in zip(expf, outf):
+#             assert line_exp == line_out
+#     os.remove(os.path.join(lst_dir, name + ".lst"))
+#     os.remove(os.path.join(lst_dir, name + ".prt"))
+#     os.remove(os.path.join(lst_dir, name + ".fna"))
+#     os.remove(os.path.join(lst_dir, name + ".gen"))
+#     os.remove(os.path.join(lst_dir, name + ".gff"))
+#     os.remove(gpath)
+
+
+# def test_format1genome_problemgen():
+#     """
+#     Test that formatting a genome (making .prt, .gen, .fna, .lst) returns an error message
+#     and does not create any output file if there is a problem while converting the
+#     .ffn to .gen
+#     """
+#     logger = my_logger()
+#     gpath = os.path.join("test", "data", "annotate", "genomes",
+#                          "B2_A3_5.fasta-problems.fna-short-contig.fna")
+#     name = "test.0417.00002"
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".tbl")
+#     tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".tbl")
+#     shutil.copyfile(tbl_init, tblout)
+#     gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".gff")
+#     gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".gff")
+#     shutil.copyfile(gff_init, gffout)
+#     lst_dir = os.path.join("test", "data", "annotate")
+#     prot_dir = lst_dir
+#     gene_dir = lst_dir
+#     rep_dir = lst_dir
+#     gff_dir = lst_dir
+#     assert not ffunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir,
+#                                        gene_dir, rep_dir, gff_dir, logger[1])
+#     # Check that all files were not created
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".lst"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".fna"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".prt"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".gen"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".gff"))
+#     msg = ("Unknown header format >EPKOMDHM_i00002 hypothetical protein in "
+#            "test/data/annotate/exp_files/B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes/"
+#            "test.0417.00002.ffn.\n"
+#            "Gen file will not be created.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+#     # remove tblout which was copied for this test
+#     os.remove(tblout)
+#     os.remove(gffout)
+
+
+# def test_format1genome_problemprt():
+#     """
+#     Test that formatting a genome (making .prt, .gen, .fna, .lst) works, with a genome
+#     which did not change name between prokka run and format step.
+#     """
+#     logger = my_logger()
+#     gpath = os.path.join("test", "data", "annotate", "genomes",
+#                          "B2_A3_5.fasta-problems.fna-short-contig.fna")
+#     name = "test.0417.00002"
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     # copy tbl without errors to error prokka dir
+#     tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".tbl")
+#     tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".tbl")
+#     shutil.copyfile(tbl_init, tblout)
+#     # copy gff without errors to error prokka dir
+#     gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".gff")
+#     gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".gff")
+#     shutil.copyfile(gff_init, gffout)
+#     # copy ffn without error to error prokka dir
+#     ffn_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".ffn")
+#     ffn_ok = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".ffn")
+#     ffn_error = ffn_ok + "-error"
+#     # change name of ffn file with error to keep it for later (used for tests)
+#     shutil.copyfile(ffn_ok, ffn_error)
+#     # copy ffn without error to prokka res (erasing ffn with error)
+#     shutil.copyfile(ffn_init, ffn_ok)
+#     lst_dir = os.path.join("test", "data", "annotate")
+#     prot_dir = lst_dir
+#     gene_dir = lst_dir
+#     rep_dir = lst_dir
+#     gff_dir = lst_dir
+#     assert not ffunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir,
+#                                        gene_dir, rep_dir, gff_dir, logger[1])
+#     # Check that all files were not created
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".lst"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".fna"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".prt"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".gen"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".gff"))
+#     msg = ("Unknown header format >EPKOMDHM00003 hypothetical protein in "
+#            "test/data/annotate/exp_files/B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes/"
+#            "test.0417.00002.faa. "
+#            "Error: invalid literal for int() with base 10: '>EPKOMDHM00003'\n"
+#            "Prt file not created from test/data/annotate/exp_files/"
+#            "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes/test.0417.00002.faa.")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+#     # remove files which were copied for this test (tblout). And rename ffn with errors
+#     # to its original name.
+#     os.rename(ffn_error, ffn_ok)
+#     os.remove(tblout)
+#     os.remove(gffout)
+
+
+# def test_format1genome_problemgff():
+#     """
+#     Test that formatting a genome (making .prt, .gen, .fna, .lst) returns an error message
+#     and does not create any output file if there is a problem while converting the
+#     .ffn to .gen
+#     """
+#     logger = my_logger()
+#     gpath = os.path.join("test", "data", "annotate", "genomes",
+#                          "B2_A3_5.fasta-problems.fna-short-contig.fna")
+#     name = "test.0417.00002"
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".tbl")
+#     tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".tbl")
+#     shutil.copyfile(tbl_init, tblout)
+#     gff_init = os.path.join("test", "data", "annotate", "test_files", "prokka_out_gff-error.gff")
+#     gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".gff")
+#     shutil.copyfile(gff_init, gffout)
+#     lst_dir = os.path.join("test", "data", "annotate")
+#     prot_dir = lst_dir
+#     gene_dir = lst_dir
+#     rep_dir = lst_dir
+#     gff_dir = lst_dir
+#     assert not ffunc.format_one_genome(gpath, name, prok_path, lst_dir, prot_dir,
+#                                        gene_dir, rep_dir, gff_dir, logger[1])
+#     # Check that all files were not created
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".lst"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".fna"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".prt"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".gen"))
+#     assert not os.path.isfile(os.path.join(lst_dir, name + ".gff"))
+#     msg = ("Problem with your gff file. '##FASTA' is not a gff entry line, whereas it should "
+#            "correspond to '11249\t12328\tD\tCDS\ttest.0417.00002.i0002_00016\tNA\t"
+#            "| hypothetical protein | NA | NA'")
+#     q = logger[0]
+#     assert q.qsize() == 1
+#     assert q.get().message == msg
+#     # remove tblout which was copied for this test
+#     os.remove(tblout)
+#     os.remove(gffout)
+
+
+# def test_format_all():
+#     """
+#     Test that when giving a list of genomes, for which prokka ran without problem,
+#     they are formatted, with all expected files created.
+#     """
+#     # genomes = {genome: [name, gpath, size, nbcont, l90]}
+#     initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
+#     initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
+#     gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
+#     onames = ["test_runprokka_H299", "test.0417.00002"]
+#     gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
+#     for f1, f2 in zip(initpaths, gpaths):
+#         shutil.copyfile(f1, f2)
+#     genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
+#                gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
+#                }
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     res_path = os.path.join("test", "data", "annotate")
+#     results = {gname: True for gname in gnames}
+#     skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path,
+#                                                    prok_path, threads=4)
+#     assert skipped == []
+#     assert skipped_format == []
+#     lstfiles = [os.path.join(res_path, "LSTINFO", name + ".lst") for name in onames]
+#     prtfiles = [os.path.join(res_path, "Proteins", name + ".prt") for name in onames]
+#     genfiles = [os.path.join(res_path, "Genes", name + ".gen") for name in onames]
+#     repfiles = [os.path.join(res_path, "Replicons", name + ".fna") for name in onames]
+#     gfffiles = [os.path.join(res_path, "gff3", name + ".gff") for name in onames]
+#     for f in lstfiles + prtfiles + genfiles + repfiles + gfffiles:
+#         assert os.path.isfile(f)
+#     shutil.rmtree(os.path.join(res_path, "LSTINFO"))
+#     shutil.rmtree(os.path.join(res_path, "Proteins"))
+#     shutil.rmtree(os.path.join(res_path, "Genes"))
+#     shutil.rmtree(os.path.join(res_path, "Replicons"))
+#     shutil.rmtree(os.path.join(res_path, "gff3"))
+#     for f in gpaths:
+#         os.remove(f)
+
+
+# def test_format_all_result_false():
+#     """
+#     Test that when giving a list of 2 genomes, 1 for which prokka ran without problem,
+#     1 for which prokka had problems (given with False in results),
+#     the correct genome is formatted, with all
+#     expected files created, and the genome with problems is not formatted.
+#     """
+#     # genomes = {genome: [name, gpath, size, nbcont, l90]}
+#     initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
+#     initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
+#     gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
+#     onames = ["test_runprokka_H299", "test.0417.00002"]
+#     gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
+#     for f1, f2 in zip(initpaths, gpaths):
+#         shutil.copyfile(f1, f2)
+#     genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
+#                gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
+#                }
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     res_path = os.path.join("test", "data", "annotate")
+#     results = {gnames[0]: True, gnames[1]: False}
+#     skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
+#     assert skipped == ["B2_A3_5.fasta-changeName.fna-short-contig.fna"]
+#     assert skipped_format == []
+#     lstfiles = os.path.join(res_path, "LSTINFO")
+#     prtfiles = os.path.join(res_path, "Proteins")
+#     genfiles = os.path.join(res_path, "Genes")
+#     repfiles = os.path.join(res_path, "Replicons")
+#     gfffiles = os.path.join(res_path, "gff3")
+#     assert os.path.isfile(os.path.join(lstfiles, onames[0] + ".lst"))
+#     assert not os.path.isfile(os.path.join(lstfiles, onames[1] + ".lst"))
+#     assert os.path.isfile(os.path.join(prtfiles, onames[0] + ".prt"))
+#     assert not os.path.isfile(os.path.join(prtfiles, onames[1] + ".prt"))
+#     assert os.path.isfile(os.path.join(genfiles, onames[0] + ".gen"))
+#     assert not os.path.isfile(os.path.join(genfiles, onames[1] + ".gen"))
+#     assert os.path.isfile(os.path.join(repfiles, onames[0] + ".fna"))
+#     assert not os.path.isfile(os.path.join(repfiles, onames[1] + ".fna"))
+#     assert os.path.isfile(os.path.join(gfffiles, onames[0] + ".gff"))
+#     assert not os.path.isfile(os.path.join(gfffiles, onames[1] + ".gff"))
+#     shutil.rmtree(os.path.join(res_path, "LSTINFO"))
+#     shutil.rmtree(os.path.join(res_path, "Proteins"))
+#     shutil.rmtree(os.path.join(res_path, "Genes"))
+#     shutil.rmtree(os.path.join(res_path, "Replicons"))
+#     shutil.rmtree(os.path.join(res_path, "gff3"))
+#     for f in gpaths:
+#         os.remove(f)
+
+
+# def test_format_all_not_result():
+#     """
+#     Test that when giving a list of 2 genomes, but only 1 is in the results list (and prokka ran
+#     without problems for it), the correct genome is formatted, with all
+#     expected files created, and the other genome is not formatted, and does not appear in
+#     skipped list (as it was removed from the study before annotation step, probably by QC).
+#     """
+#     # genomes = {genome: [name, gpath, size, nbcont, l90]}
+#     initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
+#     initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
+#     gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-changeName.fna-short-contig.fna"]
+#     onames = ["test_runprokka_H299", "test.0417.00002"]
+#     gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
+#     for f1, f2 in zip(initpaths, gpaths):
+#         shutil.copyfile(f1, f2)
+#     genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
+#                gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
+#                }
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     res_path = os.path.join("test", "data", "annotate")
+#     results = {gnames[0]: True}
+#     skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
+#     assert skipped == []
+#     assert skipped_format == []
+#     lstfiles = os.path.join(res_path, "LSTINFO")
+#     prtfiles = os.path.join(res_path, "Proteins")
+#     genfiles = os.path.join(res_path, "Genes")
+#     repfiles = os.path.join(res_path, "Replicons")
+#     gfffiles = os.path.join(res_path, "gff3")
+#     assert os.path.isfile(os.path.join(lstfiles, onames[0] + ".lst"))
+#     assert not os.path.isfile(os.path.join(lstfiles, onames[1] + ".lst"))
+#     assert os.path.isfile(os.path.join(prtfiles, onames[0] + ".prt"))
+#     assert not os.path.isfile(os.path.join(prtfiles, onames[1] + ".prt"))
+#     assert os.path.isfile(os.path.join(genfiles, onames[0] + ".gen"))
+#     assert not os.path.isfile(os.path.join(genfiles, onames[1] + ".gen"))
+#     assert os.path.isfile(os.path.join(repfiles, onames[0] + ".fna"))
+#     assert not os.path.isfile(os.path.join(repfiles, onames[1] + ".fna"))
+#     assert os.path.isfile(os.path.join(gfffiles, onames[0] + ".gff"))
+#     assert not os.path.isfile(os.path.join(gfffiles, onames[1] + ".gff"))
+#     shutil.rmtree(os.path.join(res_path, "LSTINFO"))
+#     shutil.rmtree(os.path.join(res_path, "Proteins"))
+#     shutil.rmtree(os.path.join(res_path, "Genes"))
+#     shutil.rmtree(os.path.join(res_path, "Replicons"))
+#     shutil.rmtree(os.path.join(res_path, "gff3"))
+#     for f in gpaths:
+#         os.remove(f)
+
+#         # probleme avec .fna de onames[0] qui n'est pas créé...
+
+
+# def test_format_all_error():
+#     """
+#     Test that when giving a list of 2 genomes, prokka ran without problem for both.
+#     But a problem appears while formatting the 2nd one. So, the 2nd one is not formatted,
+#     and appears in skipped_format. The first one is formated, and check that all
+#     output files are created.
+#     """
+#     # genomes = {genome: [name, gpath, size, nbcont, l90]}
+#     name = "test.0417.00002"
+#     initnames = ["H299_H561.fasta", "B2_A3_5.fasta-changeName.fna"]
+#     initpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in initnames]
+#     gnames = ["H299_H561.fasta-short-contig.fna", "B2_A3_5.fasta-problems.fna-short-contig.fna"]
+#     onames = ["test_runprokka_H299", "test.0417.00002"]
+#     gpaths = [os.path.join("test", "data", "annotate", "genomes", name) for name in gnames]
+#     for f1, f2 in zip(initpaths, gpaths):
+#         shutil.copyfile(f1, f2)
+#     genomes = {gnames[0]: [onames[0], gpaths[0], 12656, 3, 1],
+#                gnames[1]: [onames[1], gpaths[1], 456464645, 5, 1]
+#                }
+#     prok_path = os.path.join("test", "data", "annotate", "exp_files")
+#     res_path = os.path.join("test", "data", "annotate")
+#     tbl_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".tbl")
+#     tblout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".tbl")
+#     shutil.copyfile(tbl_init, tblout)
+#     gff_init = os.path.join(prok_path, "B2_A3_5.fasta-split5N.fna-short-contig.fna-prokkaRes",
+#                             name + ".gff")
+#     gffout = os.path.join(prok_path, "B2_A3_5.fasta-problems.fna-short-contig.fna-prokkaRes",
+#                           name + ".gff")
+#     shutil.copyfile(gff_init, gffout)
+#     results = {gnames[0]: True, gnames[1]: True}
+#     skipped, skipped_format = ffunc.format_genomes(genomes, results, res_path, prok_path)
+#     assert skipped == []
+#     assert skipped_format == ["B2_A3_5.fasta-problems.fna-short-contig.fna"]
+#     lstfiles = os.path.join(res_path, "LSTINFO")
+#     prtfiles = os.path.join(res_path, "Proteins")
+#     genfiles = os.path.join(res_path, "Genes")
+#     repfiles = os.path.join(res_path, "Replicons")
+#     gfffiles = os.path.join(res_path, "gff3")
+#     assert os.path.isfile(os.path.join(lstfiles, onames[0] + ".lst"))
+#     assert not os.path.isfile(os.path.join(lstfiles, onames[1] + ".lst"))
+#     assert os.path.isfile(os.path.join(prtfiles, onames[0] + ".prt"))
+#     assert not os.path.isfile(os.path.join(prtfiles, onames[1] + ".prt"))
+#     assert os.path.isfile(os.path.join(genfiles, onames[0] + ".gen"))
+#     assert not os.path.isfile(os.path.join(genfiles, onames[1] + ".gen"))
+#     assert os.path.isfile(os.path.join(repfiles, onames[0] + ".fna"))
+#     assert not os.path.isfile(os.path.join(repfiles, onames[1] + ".fna"))
+#     assert os.path.isfile(os.path.join(gfffiles, onames[0] + ".gff"))
+#     assert not os.path.isfile(os.path.join(gfffiles, onames[1] + ".gff"))
+#     shutil.rmtree(os.path.join(res_path, "LSTINFO"))
+#     shutil.rmtree(os.path.join(res_path, "Proteins"))
+#     shutil.rmtree(os.path.join(res_path, "Genes"))
+#     shutil.rmtree(os.path.join(res_path, "Replicons"))
+#     shutil.rmtree(os.path.join(res_path, "gff3"))
+#     os.remove(tblout)
+#     os.remove(gffout)
+#     for f in gpaths:
+#         os.remove(f)
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